TB-Profiler result

Run: SRR6785267
Summary

Run ID: SRR6785267

Sample name:

Date: 2024-10-03T20:52:34.660323

Number of reads: 2294590

Percentage reads mapped: 82.17

Median coverage: 54.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.97
lineage2.2 East-Asian (Beijing) RD105;RD207 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 645 c.645A>C synonymous_variant 0.17 isoniazid Not assoc w R - Interim
dnaA 649 c.649C>T synonymous_variant 0.15 isoniazid Not assoc w R - Interim
dnaA 654 c.654A>G synonymous_variant 0.15 isoniazid
dnaA 660 c.660G>C synonymous_variant 0.15 isoniazid Not assoc w R - Interim
dnaA 669 c.669C>T synonymous_variant 0.13 isoniazid
dnaA 1191 c.1191T>C synonymous_variant 0.13 isoniazid
gyrB 6238 c.999G>A synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6242 p.Arg335Lys missense_variant 0.19 levofloxacin
moxifloxacin
gyrB 6250 c.1011A>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6256 c.1017G>A synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7442 c.141G>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 7451 c.150C>G synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.16 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7541 c.240C>G synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8090 c.789C>A synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8096 c.795T>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8111 c.810G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8121 c.820T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8129 c.828T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8135 c.834C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8528 c.1227G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8543 c.1242C>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8546 c.1245T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9230 c.1929T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9233 c.1932C>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.98 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575719 c.372C>T synonymous_variant 0.13 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.9 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.94 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
hadA 732337 c.408G>A synonymous_variant 0.15 isoniazid
rpoB 760101 c.295T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760112 c.306T>C synonymous_variant 0.15 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.15 rifampicin Uncertain significance
rpoB 760139 c.333A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760142 c.336C>G synonymous_variant 0.15 rifampicin
rpoB 760181 c.375T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.14 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760376 p.Asp190Glu missense_variant 0.16 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.15 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.14 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.15 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761373 p.Val523His missense_variant 0.14 rifampicin
rpoB 761408 c.1602G>C synonymous_variant 0.14 rifampicin
rpoB 761588 c.1782C>T synonymous_variant 0.13 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.17 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762008 c.2202C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.14 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.17 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.14 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.13 rifampicin
rpoB 762167 c.2361T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 763148 c.-222G>C upstream_gene_variant 0.15 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.13 rifampicin
rpoC 763190 c.-180C>T upstream_gene_variant 0.15 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.28 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.14 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.14 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.16 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.2 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.2 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.19 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.15 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.21 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.2 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.21 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.22 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.21 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.2 rifampicin
rpoC 763936 c.567C>G synonymous_variant 0.19 rifampicin
rpoC 763939 c.570G>A synonymous_variant 0.2 rifampicin
rpoC 763942 c.573C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.14 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.14 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.14 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.14 rifampicin
rpoC 764932 c.1563C>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.18 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 765034 c.1665T>C synonymous_variant 0.13 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.17 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.15 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.15 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.2 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766010 c.2641_2642delTCinsAG synonymous_variant 0.17 rifampicin
rpoC 766021 c.2652G>C synonymous_variant 0.16 rifampicin
rpoC 766027 c.2658G>C synonymous_variant 0.16 rifampicin
rpoC 766043 p.Gln892Glu missense_variant 0.15 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 0.92 rifampicin Not assoc w R
rpoC 766801 c.3432C>G synonymous_variant 0.19 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781700 c.141G>C synonymous_variant 0.14 streptomycin
rpsL 781703 c.144G>T synonymous_variant 0.14 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.15 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.15 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.14 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.16 streptomycin
rpsL 781772 c.213C>A synonymous_variant 0.16 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.16 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.17 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.2 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.14 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.14 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.16 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.16 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.16 streptomycin
rpsL 781877 c.318T>C synonymous_variant 0.16 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.21 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.18 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.16 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.15 streptomycin Uncertain significance
rplC 800703 c.-106T>C upstream_gene_variant 0.14 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.19 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.19 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.18 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.21 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.17 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303920 c.990C>T synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1304893 p.Gly655Ser missense_variant 0.12 pretomanid
delamanid
clofazimine
fbiC 1304910 c.1980G>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1304916 c.1986T>C synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304928 c.1998T>C synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fbiC 1304937 c.2007G>C synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304958 c.2028T>G synonymous_variant 0.14 pretomanid
delamanid
clofazimine
sigE 1364706 c.294G>A synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.95 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.13 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.22 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673710 c.-492C>A upstream_gene_variant 0.15 isoniazid
ethionamide
inhA 1673716 c.-486_-485delGCinsAA upstream_gene_variant 0.17 isoniazid
ethionamide
rpsA 1833661 c.120A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.19 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.18 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.96 pyrazinamide Not assoc w R - Interim
rpsA 1834303 c.762T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834618 c.1077G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.19 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.17 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834733 p.Ala398Ser missense_variant 0.14 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834753 c.1212T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.13 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2101920 c.1123A>C synonymous_variant 0.14 isoniazid
delamanid
ethionamide
ndh 2101924 c.1119T>G synonymous_variant 0.14 isoniazid
delamanid
ethionamide
ndh 2103088 c.-46T>G upstream_gene_variant 0.98 isoniazid Uncertain significance
delamanid
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2782948 c.1095A>G synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782957 c.1086A>G synonymous_variant 0.14 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2782966 c.1077C>A synonymous_variant 0.18 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782969 c.1074A>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782972 c.1071G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782981 c.1062G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783656 c.387G>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783860 c.183T>C synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783863 c.180C>T synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783883 c.160T>C synonymous_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783884 c.159T>C synonymous_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783887 c.156C>G synonymous_variant 0.29 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
thyX 3067601 p.Arg115His missense_variant 0.26 para-aminosalicylic_acid
thyX 3067611 p.Lys112Thr missense_variant 0.31 para-aminosalicylic_acid
thyX 3067619 c.327A>C synonymous_variant 0.31 para-aminosalicylic_acid
thyX 3067631 c.315C>G synonymous_variant 0.31 para-aminosalicylic_acid
thyX 3067634 c.312C>G synonymous_variant 0.31 para-aminosalicylic_acid
thyX 3067652 c.294T>C synonymous_variant 0.28 para-aminosalicylic_acid
thyX 3067661 c.285C>G synonymous_variant 0.28 para-aminosalicylic_acid
thyX 3067685 c.261A>C synonymous_variant 0.29 para-aminosalicylic_acid
thyX 3067691 p.Ile85Leu missense_variant 0.28 para-aminosalicylic_acid
thyX 3067694 c.252G>C synonymous_variant 0.3 para-aminosalicylic_acid
thyX 3067718 c.228C>G synonymous_variant 0.27 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.28 para-aminosalicylic_acid
thyX 3067727 c.219A>C synonymous_variant 0.27 para-aminosalicylic_acid
thyX 3067793 c.153T>C synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067799 c.147G>A synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067802 c.144C>G synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067814 c.132T>C synonymous_variant 0.18 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625624 c.-714C>G upstream_gene_variant 0.18 rifampicin
bedaquiline
mtrB 3625636 c.978C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625797 p.Val273Met missense_variant 0.14 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626774 c.-163_-161delAGGinsCGC upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3626783 c.-170C>G upstream_gene_variant 0.18 rifampicin
bedaquiline
mtrA 3626786 c.564A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3626792 c.558G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626795 c.-182C>T upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3626798 c.-185T>C upstream_gene_variant 0.19 rifampicin
bedaquiline
mtrA 3626804 c.546A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626840 c.-227C>G upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrA 3626846 c.504G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626858 c.-245A>G upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrB 3626861 c.-248C>G upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3626866 c.-253T>C upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrB 3626876 c.-263A>G upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3626885 c.-272A>C upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrB 3626890 c.-277T>C upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3626903 c.-290T>C upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrB 3626912 c.-299T>G upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrB 3626957 c.-344G>C upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrB 3627008 c.-395G>C upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3627011 c.-398T>G upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrB 3627074 c.-461G>C upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrA 3627080 c.270T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627083 c.-470G>C upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrA 3627098 c.252A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3878947 c.-440G>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878962 c.-455G>A upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878968 c.-461T>C upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3878976 c.-469A>G upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.2 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.21 rifampicin Uncertain significance
rpoA 3879079 c.-572A>G upstream_gene_variant 0.16 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.16 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.15 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.15 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.15 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.15 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.14 rifampicin
rpoA 3879178 c.-671T>C upstream_gene_variant 0.14 rifampicin
clpC1 4039397 c.1308A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.14 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.14 pyrazinamide
clpC1 4040363 c.342A>T synonymous_variant 0.14 pyrazinamide
clpC1 4040369 c.336C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040380 c.325T>C synonymous_variant 0.14 pyrazinamide
clpC1 4040393 c.312G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040411 c.294T>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
clpC1 4040423 c.282A>G synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
clpC1 4040426 c.279T>C synonymous_variant 0.24 pyrazinamide
clpC1 4040431 c.274T>C synonymous_variant 0.3 pyrazinamide
clpC1 4040444 c.261C>T synonymous_variant 0.32 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
clpC1 4040459 c.246C>G synonymous_variant 0.29 pyrazinamide
clpC1 4040465 c.240T>C synonymous_variant 0.28 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4040477 c.228G>C synonymous_variant 0.25 pyrazinamide
clpC1 4040480 c.225T>G synonymous_variant 0.26 pyrazinamide
clpC1 4040501 c.204C>T synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4040522 c.183T>C synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4040528 c.177G>C synonymous_variant 0.23 pyrazinamide
clpC1 4040531 c.174T>C synonymous_variant 0.21 pyrazinamide
clpC1 4040534 c.171A>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4040537 c.168G>C synonymous_variant 0.2 pyrazinamide
clpC1 4040546 c.159G>C synonymous_variant 0.18 pyrazinamide
clpC1 4040551 c.154T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
panD 4044725 c.-444C>T upstream_gene_variant 0.13 pyrazinamide
glpK 4138670 c.1086G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.98 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R